[gmx-users] (no subject)
lindahl at csb.stanford.edu
Wed Mar 31 15:11:02 CEST 2004
1. You are comparing two different dihedrals. One is specifically for
the atoms CA-CA-C-N, while the other one is a wildcarded type - they
are NOT necessarily identical.
2. The dihedrals in amber are probably for the old version of
united-atom OPLS.... Even the OPLS-AA values changed a bit between 1996
(first publication) and 2002.
In general, we'd definitely look into it if there are any discrepancies
with the published numbers of OPLS-AA/L (although I've already checked
that pretty carefully), but I don't have time to debug amber :-)
On Mar 31, 2004, at 2:30 PM, Nikita Polyakov wrote:
> Hello all!
> I'm trying to convert Amber dihedral constants to ffoplsaabon.itp.
> I took opls_parm.dat from Amber7 force field and extact that line for
> X -CK-CB-X 4 5.3 180. 2. Supposed dihedral
> In that case probably C0 = -C2 = 5.565. So C1=C3=C4=C5=0
> X CA C X 3 5.565 0.00000 5.565
> 0.00000 0.00000 0.00000 But in ffoplsaabon.itp for example:
> CA CA C N 3 4.60548 0.00000 -4.60548
> 0.00000 0.00000 0.00000 ; benzamide Could you explain difference
> or where I did mistake?
> Nikita Polyakov, MSU student.
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